Thank you both very much. Yes fortunately I'm running on Linux (well, it's bash on windows). The unu command for unzipped output worked, and now I'm running the zipped version (see code below, it's taking much longer, still running)

Can I confirm with you that the code I'm runningn for DWIConvert is still accurate, given the new Slicer 4.8? (see below)

## Running DWIConvert to go from nii to nrrd
$SlicerNew --launch DWIConvert --inputVolume ${origDWI}.nii.gz --conversionMode FSLToNrrd --inputBValues ${bval}.txt --inputBVectors ${bvec}.txt --outputVolume ${nrrdraw}.nrrd

## Using the unu command
$SlicerOld --launch unu convert -t short -clamp -i ${DTIPREPDIR}/${SUBJ}_dwi_QCed.nrrd | $SlicerOld --launch unu save -e gzip -f nrrd -o ${DTIPREPDIR}/${SUBJ}_dwi_QCed_unu.nrrd

## Running the DWIConvert take unu output and go from nrrd to nii
$SlicerNew --launch DWIConvert --inputVolume ${nrrdraw}_QCed_unu.nrrd --conversionMode NrrdToFSL --outputBValues ${bval}_QCed.txt --outputBVectors ${bvec}_QCed.txt --outputVolume ${nrrdraw}_QCed.nii.gz

Another strange thing is that now I cannot run this code from my original .sh script (it only works on the command line), from the script produces the error below:

--launch: command not found

Have you seen this before?

Is it possible it's because I deleted the NA-MIC settings folder? (as instructed on the website, copied below)

[On Linux, remove the directory where the application is located. To clean up settings, remove "~/.config/NA-MIC/"]